Dear BioPerl community,
I developed this application for a research lab here at the University of Missouri. I was wondering if this sounded okay and if it were okay to use the "Bio" namespace.
Thank you for all you do.
Sincerely,
Christopher Bottoms
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SYNOPSIS
perl perl5/lib/perl5/Bio/App/SELEX/RNAmotifAnalysis.pm --infile simple.seqs --cpus 4 --run
DESCRIPTION
This module pipelines steps in the analysis of SELEX (Systematic Evolution
of Ligands through EXponential enrichment) data.
This main module creates scripts to do the following:
(1) Cluster similar sequences based on edit distance.
(2) Align sequences within each cluster (using mafft).
(3) Calculate the secondary structure of the aligned sequences (using
RNAalifold, from the Vienna RNA package)
(4) Build covariance models using cmbuild from Infernal.
The module Bio::App::SELEX::CovarianceSearch can also be used to create
scripts for doing iterative refinements of covariance models.
EXAMPLE USE
perl perl5/lib/perl5/Bio/App/SELEX/RNAmotifAnalysis.pm --infile simple.seqs --cpus 4 --run
(The file 'simple.seqs' should only contain sequences, one per line.)
This will cluster the sequences found in 'simple.seqs' and create a FASTA
file for each one. The FASTA files will be grouped into batches (i.e. one
per cpu requested) that will be placed in a separate directory for each
batch, and processed within that directory. At the end of processing, for
each cluster there will be a covariance model and postscript illustration
files. The batch script used to process each batch will be located in the
respective batch directory. To produce the scripts without running them,
simply exclude the --run flag from the command line.
CONFIGURATION AND ENVIRONMENT
As written, this code makes heavy use of UNIX utilities and is
therefore only supported on UNIX-like environemnts (e.g. Linux, UNIX, Mac
OS X).
Install Infernal, MAFFT, and the RNA Vienna package ahead of time and add
the directories containing their executables to your PATH, so that the
first time you run RNAmotifAnalysis.pm a configuration file (cluster.cfg)
will be generated for you with all of the correct parameters. Otherwise,
you'll need to update your cluster.cfg file manually.
After installing mafft, Infernal, and Vienna RNA packages, add the
directories in which their executables reside in your PATH.
For example, assuming that the mafft executable is located in the directory
'/usr/local/myapps/bin/', you would want to add it to your PATH. To make
sure this is done every time you open a terminal window, add this to your
.bashrc file, thus:
echo 'export PATH=/usr/local/myapps/bin:$PATH' >> ~/.bashrc.
Then, to make it effective immediately, you can source your .bashrc file:
source ~/.bashrc
INSTALLATION
These installation instructions assume being able to open and use a
terminal window on Linux.
(0) Some systems need several dependencies installed ahead of time.
You may be able to skip this step. However, if subsequent steps don't
work, then be sure that some basic libraries are installed, as shown
below (or ask a system administrator to take care of it):
For RedHat or CentOS 5.x systems (tested on CentOS 5.5)
Open a terminal and then type the following command, answering all
questions in the afirmative:
sudo yum install gcc
For RedHat or CentOS 6.x systems (tested on CentOS 6.3)
Open a terminal and then type the following commands, answering
all questions in the afirmative:
sudo yum install gcc
sudo yum install perl-devel
For Debian or Ubuntu systems (tested on Debian 5.06, Ubuntu 12-04 LTS)
Open a terminal and then type the following commands, answering
all questions in the afirmative:
sudo apt-get install gcc
sudo apt-get install make
(1) Install the non-Perl dependencies:
(Versions shown are those that we've tested. Please contact us if
newer versions do not work.)
Infernal 1.0.2 (http://infernal.janelia.org/)
MAFFT 6.849b (http://mafft.cbrc.jp/alignment/software/)
RNA Vienna package 1.8.4 (http://www.tbi.univie.ac.at/~ivo/RNA/)
(2) Either (a) download and run our installer or (b) use a CPAN client
to install Bio::App::SELEX::RNAmotifAnalysis. Note that our installer
creates the directory 'perl5' inside your home directory. This
directory is for holding Perl modules, including this module and any
Perl module dependencies not already included on your system. The
installer also appends commands to your .bashrc file to make it easy
for the Perl runtime to find these new modules (i.e. it includes your
local 'perl5/lib/perl5' directory in the PERL5LIB environment
variable).
(a) Use the installer
i. Download installer (and name it "installer")
curl -o installer -L http://ircf.rnet.missouri.edu:8000/share.attachment/184
ii. Make it executable
chmod u+x installer
iii. Run it. In a few cases (e.g. CentOS 5.5) we've had to run the
installer as many as three times to get all of the Perl
modules installed. Please contact us if this doesn't work
after three attempts.
./installer
(b) If you prefer using a CPAN client, then we recommend that you install
Bio::App::SELEX::RNAmotifAnalyis 'locally' instead of to system
perl, to avoid overwriting core Perl modules. If this doesn't make
sense to you, then please be sure to use the installer as
described in (a) above.
INCOMPATIBILITIES
None known
BUGS AND LIMITATIONS
There are no known bugs in this module.
Please report problems to molecules <at> cpan <dot> org
Patches are welcome.
RELATED PUBLICATIONS
Ditzler et. al. Manuscript currently in review.